The analysis is summarized in the CATS_rb_comparison.html HTML file.
An example of the HTML output is provided here
Note on transcriptome assembly order and names: Assemblies will appear in the order they were provided on the command line when running the tool. For visualization purposes, assembly names are limited to a maximum of 20 characters; names exceeding this limit will be truncated. If multiple assemblies share the same name, a numeric suffix (e.g., .1, .2, etc.) will be appended to distinguish these assemblies.
CATS-rb produces several summary files encompassing transcriptome assembly length statistics, various mapping metrics, and completeness analysis results:
CATS_rb_general_statistics.tsv: contains descriptive statistics of transcript length (mean, median, interquartile range, range, N50, L50, N90, L90( and GC content.
CATS_rb_main_comparison_results.tsv: contains transcriptome assembly mapping metrics and the results of relative completeness analysis.
CATS_rb_annotation_based_analysis_results.tsv: contains the results of annotation-based completeness analysis. This table is provided only if annotation-based analysis is enabled.
CATS-rb produces several figures, providing a detailed visualization of CATS-rb quality metrics.
transcript_length visualizes the distribution of transcript length.
transcript_alignment_proportion visualizes the distribution of transcript alignment proportion.
number_of_exons_per_transcript visualizes the distribution of exon number per transcript.
exon_length visualizes the distribution of exon length.
exon_set_genomic_distribution visualizes the positional distribution of exon sets in the analysed genome.
number_of_isoforms_per_transcript_set visualizes the distribution of isoform number per transcript set.
exon_set_length and transcript_set_length visualize the distribution of exon/transcript set length.
common_exon_set_length and common_transcript_set_length visualize the distribution of common exon/transcript set length. Common sets correspond to set groups found in all analysed transcriptome assemblies.
common_exon_set_relative_length and common_transcript_set_relative_length visualize the distribution of common exon/transcript set relative length. Relative length is calculated with respect to the longest set within each group of common sets.
unique_exon_set_length and unique_transcript_set_length visualize the distribution of unique exon/transcript set length. Unique sets correspond to sets found in only one of the analysed transcriptome assemblies.
exon_set_upset_plot.pdf and transcript_set_upset_plot.pdf visualize UpSet plots for exon/transcript sets. Each UpSet plot is accompanied by two boxplots: the upper boxplot illustrates the length distribution of exon/transcript sets within each subset, while the lower boxplot displays the distribution of the ratio between the minimum and maximum exon/transcript set length within each subset.
exon_set_pairwise_comp_similarity_tileplot and transcript_set_pairwise_comp_similarity_tileplot visualize the exon/transcript set pairwise completeness similarity tileplot between the analysed transcriptome assemblies. Completeness similarity is defined as the mean completeness ratio of each corresponding exon/transcript set between each assembly pair.
pairwise_exon_set_venn_diagrams and pairwise_transcript_set_venn_diagrams visualize the exon/transcript set Venn diagrams for each transcriptome assembly pair. These plots are generated only if the comparison involves ten or fewer assemblies.
exon_set_heatmap.pdf and transcript_set_heatmap.pdf visualize hierarchical clustering heatmaps of transcriptome assemblies and exon/transcript sets. Assemblies (columns) are clustered based on the relative completeness of clustered exon/transcript sets (rows). Clustering is performed using complete linkage and Euclidean distance.
unique_exon_set_position_in_non_origin_transcriptomes visualizes the positional analysis of unique exon sets in non-origin transcriptome assemblies. Each unique exon set is classified as either: (1) located within a transcript set, (2) proximal to a transcript set, or (3) distant from any transcript set (in non-origin assemblies).
missing_exon_set_position visualizes the positional analysis of missing exon sets. Each missing exon set is classified as either: (1) located within a transcript set, or (2) located outside any transcript set (in the transcriptome assembly from which the exon set is missing).
prop_of_exon_set_covered_by_a_gtf_set and prop_of_transcript_set_covered_by_a_gtf_set visualize the distribution of the proportion of exon/transcript sets covered by a GTF set.
annotation_based_exon_set_upset_plot.pdf and annotation_based_transcript_set_upset_plot.pdf visualize annotation-based UpSet plots for exon/transcript sets. Each UpSet plot is accompanied by two boxplots: the upper boxplot illustrates the length distribution of exon/transcript sets within each subset, while the lower boxplot displays the distribution of the ratio between the minimum and maximum exon/transcript set length within each subset.
annotation_based_pairwise_exon_set_venn_diagrams and annotation_based_pairwise_transcript_set_venn_diagrams visualize annotation-based exon/transcript set Venn diagrams for each transcriptome assembly pair. These plots are generated only if the comparison involves ten or fewer assemblies.
annotation_based_exon_set_heatmap.pdf and annotation_based_transcript_set_heatmap.pdf visualize annotation-based hierarchical clustering heatmaps of transcriptome assemblies and exon/transcript sets. Assemblies (columns) are clustered based on the relative completeness of clustered exon/transcript sets (rows). Clustering is performed using complete linkage and Euclidean distance.
CATS-rb also produces several .tsv files containing detailed per-transcript and element set metrics:
unmapped_transcripts.tsv lists unmapped transcripts.
transcript_aln_prop.tsv contains the proportion of aligned transcript length for each transcript.
transcripts_low_aln_prop.tsv lists transcripts classified as structurally inconsistent due to low alignment rate.
transcript_mapped_N.tsv contains the number of mappings for each transcript.
transcripts_disjunct_genomic_regions.tsv lists transcripts classified as structurally inconsistent due to different transcript segments mapping to disjunct genomic regions.
str_inconsistent_transcripts.tsv lists all structurally inconsistent transcripts (unmapped + low alignment rate + segments mapping to disjunct genomic regions).
per_transcript_exon_N.tsv contains the exon number per transcript.
exon_sets.tsv and transcript_sets.tsv contain exon/transcript set coordinates.
unique_exon_sets.tsv and unique_transcript_sets.tsv contain unique exon/transcript set coordinates.
missing_exon_set_ranges.tsv contains genomic coordinate ranges of missing exon sets identified in other transcriptome assemblies. Range coordinates are defined by taking the range from minimum to maximum genomic coordinate of the exon set group in all assemblies in which the set was found.
exon_set_pairwise_completeness_similarity_matrix.tsv and transcript_set_pairwise_completeness_similarity_matrix.tsv contain exon/transcript set pairwise completeness similarity between the analysed transcriptome assemblies. Completeness similarity is defined as the mean completeness ratio of each corresponding exon/transcript set between each assembly pair.
annotation_based_exon_set_coordinates.tsv amd annotation_based_transcript_set_coordinates.tsv contain annotation-based exon/transcript set coordinates.
exon_set_annotation_based_comp_matrix.tsv and transcript_set_annotation_based_comp_matrix.tsv contain the completeness of exon/transcript sets relative to the GTF reference set.